few bug in the graph algorithm

Former-commit-id: b61bdd9f671e2f5e90d32c1beac1ed84efa5e05c

pkg/obikmer/debruijn.go

@@ -3,6 +3,7 @@ package obikmer
 import (
 	"bytes"
 	"fmt"
+	"log"
 
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 )
@@ -166,9 +167,10 @@ func (g *DeBruijnGraph) MaxNext(index uint64) (uint64, bool) {
 	max := uint(0)
 	rep := uint64(0)
 	for _, idx := range ns {
-		w, _ := g.graph[idx]
+		w := g.graph[idx]
 		if w > max {
 			rep = idx
+			max = w
 		}
 	}
 
@@ -191,33 +193,34 @@ func (g *DeBruijnGraph) MaxPath() []uint64 {
 }
 
 func (g *DeBruijnGraph) LongestPath() []uint64 {
-	var path []uint64 
+	var path []uint64
 	wmax := uint(0)
 	ok := true
 
-	starts:= g.Heads()
+	starts := g.Heads()
-
+	log.Println(starts)
-	for _,idx := range starts {
+	for _, idx := range starts {
 		lp := make([]uint64, 0, 1000)
+		ok = true
 		w := uint(0)
 		for ok {
-			nw:= g.graph[idx]
+			nw := g.graph[idx]
-			w+=nw
+			w += nw
 			lp = append(lp, idx)
 			idx, ok = g.MaxNext(idx)
 		}
-	
+
+		log.Printf("max : %d  current %d", wmax, w)
 		if w > wmax {
-			path=lp
+			path = lp
-			wmax=w
+			wmax = w
 		}
 	}
 
-
 	return path
 }
 
-func (g *DeBruijnGraph) LongestConsensus(id string) (*obiseq.BioSequence,error) {
+func (g *DeBruijnGraph) LongestConsensus(id string) (*obiseq.BioSequence, error) {
 	path := g.LongestPath()
 	s := g.DecodePath(path)
 
@@ -228,13 +231,12 @@ func (g *DeBruijnGraph) LongestConsensus(id string) (*obiseq.BioSequence,error)
 			"",
 		)
 
-		return &seq,nil
+		return &seq, nil
 	}
 
-	return nil,fmt.Errorf("cannot identify optimum path")
+	return nil, fmt.Errorf("cannot identify optimum path")
 }
 
-
 func (g *DeBruijnGraph) Heads() []uint64 {
 	rep := make([]uint64, 0, 10)
 
@@ -281,13 +283,13 @@ func (g *DeBruijnGraph) DecodePath(path []uint64) string {
 
 		for _, idx := range path[1:] {
 			buf.WriteByte(decode[idx&3])
-		}	
+		}
 	}
 
 	return buf.String()
 }
 
-func (g *DeBruijnGraph) BestConsensus(id string) (*obiseq.BioSequence,error) {
+func (g *DeBruijnGraph) BestConsensus(id string) (*obiseq.BioSequence, error) {
 	path := g.MaxPath()
 	s := g.DecodePath(path)
 
@@ -298,10 +300,10 @@ func (g *DeBruijnGraph) BestConsensus(id string) (*obiseq.BioSequence,error) {
 			"",
 		)
 
-		return &seq,nil
+		return &seq, nil
 	}
 
-	return nil,fmt.Errorf("cannot identify optimum path")
+	return nil, fmt.Errorf("cannot identify optimum path")
 }
 
 func (g *DeBruijnGraph) Weight(index uint64) int {
@@ -374,3 +376,51 @@ func (graph *DeBruijnGraph) Push(sequence *obiseq.BioSequence) {
 	}
 
 }
+
+func (graph *DeBruijnGraph) GML() string {
+	buffer := bytes.NewBuffer(make([]byte, 0, 1000))
+
+	buffer.WriteString(
+		`graph [
+		comment "De Bruijn graph"
+		directed 1
+		
+		`)
+
+	for idx := range graph.graph {
+		node := graph.DecodeNode(idx)
+		buffer.WriteString(
+			fmt.Sprintf("node [ id \"%s\" ]\n", node),
+		)
+		n := graph.Nexts(uint64(idx))
+		if len(n) == 0 {
+			idx <<= 2
+			idx &= graph.kmermask
+			node := graph.DecodeNode(idx)
+			buffer.WriteString(
+				fmt.Sprintf("node [ id \"%s\" \n label \"%s\" ]\n", node, node),
+			)
+		}
+	}
+
+	for idx, weight := range graph.graph {
+		src := graph.DecodeNode(idx)
+		label := decode[idx&3]
+		idx <<= 2
+		idx &= graph.kmermask
+		dst := graph.DecodeNode(idx)
+
+		buffer.WriteString(
+			fmt.Sprintf(`edge [ source "%s"
+				target "%s" 
+				color "#00FF00"
+				label "%c[%d]"
+				]
+				
+				`, src, dst, label, weight),
+		)
+	}
+	buffer.WriteString("]\n")
+	return buffer.String()
+
+}

pkg/obitools/obiconsensus/obiconsensus.go

@@ -41,7 +41,7 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice, quorum float64) (*obiseq.BioSe
 	spectrum := graph.LinkSpectrum()
 	cum := make(map[int]int)
 
-	spectrum[1]=0
+	spectrum[1] = 0
 	for i := 2; i < len(spectrum); i++ {
 		spectrum[i] += spectrum[i-1]
 		cum[spectrum[i]]++
@@ -63,26 +63,36 @@ func BuildConsensus(seqs obiseq.BioSequenceSlice, quorum float64) (*obiseq.BioSe
 			break
 		}
 	}
-
+	threshold /= 2
 	graph.FilterMin(threshold)
 	log.Printf("Graph size : %d\n", graph.Len())
 
-	seq,err :=  graph.LongestConsensus(seqs[0].Source())
+	// file, err := os.Create(
+	// 	fmt.Sprintf("%s.gml", seqs[0].Source()))
+
+	// if err != nil {
+	// 	fmt.Println(err)
+	// } else {
+	// 	file.WriteString(graph.GML())
+	// 	file.Close()
+	// }
+
+	seq, err := graph.LongestConsensus(seqs[0].Source())
 
 	seq.SetCount(len(seqs))
-	seq.SetAttribute("seq_length",seq.Len())
+	seq.SetAttribute("seq_length", seq.Len())
-	seq.SetAttribute("kmer_size",kmersize)
+	seq.SetAttribute("kmer_size", kmersize)
-	seq.SetAttribute("kmer_min_occur",threshold)
+	seq.SetAttribute("kmer_min_occur", threshold)
-	seq.SetAttribute("kmer_max_occur",graph.MaxLink())
+	seq.SetAttribute("kmer_max_occur", graph.MaxLink())
-	seq.SetAttribute("filtered_graph_size",graph.Len())
+	seq.SetAttribute("filtered_graph_size", graph.Len())
-	seq.SetAttribute("full_graph_size",total_kmer)
+	seq.SetAttribute("full_graph_size", total_kmer)
 
-	return seq,err
+	return seq, err
 }
 
 func Consensus(iterator obiiter.IBioSequence, quorum float64) obiiter.IBioSequence {
 	newIter := obiiter.MakeIBioSequence()
-    size:=10
+	size := 10
 
 	newIter.Add(1)
 
@@ -97,7 +107,7 @@ func Consensus(iterator obiiter.IBioSequence, quorum float64) obiiter.IBioSequen
 
 		for iterator.Next() {
 			seqs := iterator.Get()
-			consensus,err := BuildConsensus(seqs.Slice(),quorum)
+			consensus, err := BuildConsensus(seqs.Slice(), quorum)
 
 			if err == nil {
 				buffer = append(buffer, consensus)